Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

被引：143

作者：

Castanera, Raul ^{[1
]}

Lopez-Varas, Leticia ^{[1
]}

Borgognone, Alessandra ^{[1
]}

LaButti, Kurt ^{[2
]}

Lapidus, Alla ^{[2
,3
]}

Schmutz, Jeremy ^{[2
,4
]}

Grimwood, Jane ^{[2
,4
]}

Perez, Gumer ^{[1
]}

Pisabarro, Antonio G. ^{[1
]}

Grigoriev, Igor V. ^{[2
]}

Stajich, Jason E. ^{[5
]}

Ramirez, Lucia ^{[1
]}

机构：

[1] Univ Publ Navarra, Dept Agr Prod, Genet & Microbiol Res Grp, Pamplona, Navarre, Spain

[2] US Dept Energy Joint Genome Inst, Walnut Creek, CA USA

[3] St Petersburg State Univ, Ctr Algorithm Biotechnol, St Petersburg, Russia

[4] Hudson Alpha Inst Biotechnol, Huntsville, AL USA

[5] Univ Calif Riverside, Dept Plant Pathol & Microbiol, Inst Integrat Genome Biol, Riverside, CA 92521 USA

来源：

PLOS GENETICS | 2016年 / 12卷 / 06期

基金：

美国国家科学基金会;

关键词：

MULTIPLE SEQUENCE ALIGNMENT; DE-NOVO IDENTIFICATION; INDUCED POINT MUTATION; BLACK TRUFFLE GENOME; EPIGENETIC REGULATION; SMALL RNAS; GENE; EVOLUTION; RETROTRANSPOSONS; DIVERSITY;

D O I：

10.1371/journal.pgen.1006108

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra-and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation.

引用

页数：27

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